VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Aug 02 2011 - 07:43:29 CDT

On Tue, Aug 2, 2011 at 3:12 AM, sajad falsafi <sajad.falsafi_at_yahoo.com> wrote:
> Hi,
> 1- you should modify atom type and write suitable name, for example:
> REMARK   Materials Studio PDB file
> REMARK   Created:  Mon Jun 20 09:27:35 Afghanistan Standard Time 2011
> CRYST1   16.907   16.907   14.757  90.00  90.00 120.00 P1
> ATOM      1 C001   MOL     2      13.811   6.188   0.243  1.00
> 0.00           C
> ATOM      2 C002   MOL     2      13.261   7.495   0.243  1.00
> 0.00           C
> ATOM      3 C003   MOL     2      12.887   8.098   1.473  1.00
> 0.00           C
> ATOM      4 C004   MOL     2      13.981   5.499   1.473  1.00
> 0.00           C
> ATOM      5 C005   MOL     2      11.419   9.628   0.243  1.00
> 0.00           C
>
> 2- after you should modify topology and forcefield, like this example:
> MASS    20 C     12.01100 C !
> ATOM C020 CN 0.00
> BOND C001 C002 C002 C003 C003 C004 C004 C005
> after these you can make a psf file for your pdb.

for a system like this, it would be _much_ easier to
build a topology using the topotools plugin. in fact,
the nanotube builder plugin integrated in VMD uses
it for exactly that purpose.

> if you want that, you need to hire a personal
> consultant. we can send you my hourly rates,

good luck with that. i've seen somebody that uses
free software willing to pay for this kind of advice.

cheers,
    axel.

> if you are interested.
> Hope this helps you
> Sajad & Zahra
>
> ________________________________
> From: safron saif <safron10_at_gmail.com>
> To: vmd-l_at_ks.uiuc.edu
> Sent: Monday, August 1, 2011 4:52 PM
> Subject: vmd-l: about psf file generation
>
> Dear vmd users,
>
> I am using Materials Studio software to get the structure of Carbon Nanotube
> (defective).I  got pdb file for the structure from Material Studio.I have
> created .inp file and .pgn file for creating the psf file based on this pdb
> file.I am generated the .psf file also.The problem is that the generated
> .psf file contains only one atom or i am not getting the .psf file for all
> the atoms.I couldn't understand where i went wrong.I am attaching the .pdb ,
> .inp and .pgn file for CNT with this mail.Please check it and suggest me if
> you have any idea to solve this problem.
>
>
> thanking you,
>
> safron,
>
>
>
>
> 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.